HiCcompare

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see HiCcompare.

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets


Bioconductor version: 3.13

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.

Author: John Stansfield <stansfieldjc at vcu.edu>, Kellen Cresswell <cresswellkg at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Maintainer: John Stansfield <stansfieldjc at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Citation (from within R, enter citation("HiCcompare")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HiCcompare")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HiCcompare")
HiCcompare Usage Vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews HiC, Normalization, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License MIT + file LICENSE
Depends R (>= 3.4.0), dplyr
Imports data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
System Requirements
URL https://github.com/dozmorovlab/HiCcompare
Bug Reports https://github.com/dozmorovlab/HiCcompare/issues
See More
Suggests knitr, rmarkdown, testthat, multiHiCcompare
Linking To
Enhances
Depends On Me
Imports Me multiHiCcompare, SpectralTAD, TADCompare
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HiCcompare_1.14.0.tar.gz
Windows Binary HiCcompare_1.14.0.zip
macOS 10.13 (High Sierra) HiCcompare_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCcompare
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCcompare
Bioc Package Browser https://code.bioconductor.org/browse/HiCcompare/
Package Short Url https://bioconductor.org/packages/HiCcompare/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive